// Globals.h
// 1 Dec 1995	(moved out of EstCommand/Command.h)
// Kevin Karplus

// All "globals" of the program are static members of this type
// (except the static members of other types!)

#ifndef Globals_H
#define Globals_H

using namespace std;

#include <vector>
#include <fstream>
#include <time.h>
#include <sys/time.h>

#include "NamedClass/NameToPtr.h"


// Forward References
class TrainSet;	
class InterfaceDescription;
class NeuralNet;
class NetActivation;
class NetQuality;
class OneChain;
class BackgroundProbs;
class AlphabetTuple;
class GenSequence;

class Globals
{   
    private:
        // The neural networks used for prediction or design
	static vector <NeuralNet *> NNs;
	
    public:	// static

	// add a neural net to the list if its input interface is
	// compatible with the existing networks.
	// Return 0 and don't add network 
	
	static bool add_neural_net(NeuralNet *n);
	inline static int num_nns(void)
	{    return NNs.size();
	}
	
	static inline NeuralNet *nn(int i=-1)
	{   if (i<0) i+=NNs.size();
	    if ( static_cast<int>(NNs.size()) <=i)  return NULL;
	    return NNs[i];
	}
	
	// Three sets of training data:
	//	for training the neural network:	training
	//	for monitoring the progress of the training
	//	  and selecting between parameter sets:	cross_training
	//	for the final testing of the network:	testing
	// and one set, without known correct answers:	predicting
	static TrainSet *training, *cross_training, *testing, *predicting;
	
	// which of the three sets should new input data be added to?
	static TrainSet *which_set_to_add_to;
	
	// Added by Frellsen:
	// The chains used by design-1st
	static vector <OneChain *>design_chains;
        static void clear_design_chains(void);

	// which columns of the design chain should be 
	//	copied from the provided "correct" answer.
	static vector <bool> FreezeTheseColumns;
        static void initialize_freeze(void);

	// which columns of the design chain must be 
	//	changed from the provided "correct" answer.
	static vector <bool> ChangeTheseColumns;
        static void initialize_change(void);

	// generator for random sequences, when they are needed.
	static GenSequence* SequenceGenerator;
	
	static ofstream* ReportSequenceWeightsTo;
		// where to report sequence weights after computing them

	// file to which NetQuality data will be recorded after each
	// training and cross-validation epoch
        static ofstream* ReportNetQualityForTrainTo;
        static ofstream* ReportNetQualityForCrossTrainTo;
        static ofstream* ReportNetQualityForTestTo;

	// file to which NetQuality data will be recorded after each
	// individual chain:
        static ofstream* ReportNetQualityForTrainChainTo;
        static ofstream* ReportNetQualityForCrossTrainChainTo;
        static ofstream* ReportNetQualityForTestChainTo;

	// file to which unit usage data is to be recorded 
	static ofstream* ReportUnitUsageTo;
	// file to which QvsPhat plot is to be recorded 
	static ofstream* ReportQvsPhatTo;

	// hash table for mapping alphabet names to
	//	background probabilities
	static NameToPtr BackgroundProbsByName;
	static const BackgroundProbs* background_probs(
			const AlphabetTuple*al, OptionIfNew opt=ErrorIfNew);

	
	// Times at beginning of program---need to be initialized
	// with     gettimeofday(&Globals::StartWallTime,0);
	//	    getrusage(RUSAGE_SELF, &resources)
	// at beginning of main()
	static struct timeval StartWallTime;
	static struct timeval StartCpuTime;
	
	// functions to compute the number of cpu seconds or wall-clock
	// seconds since the time stores in StartCpuTime and StartWallTime.
	static double user_seconds(void);
	static double elapsed_seconds(void);
	

        static void clear_all(void);
	// close all files and delete all data structures.
	
};


// CHANGE LOG:
// 21 July 1997 Kevin Karplus
//	copied from estimat-dist and removed everything related to
//	TestSet or regularizer stack.
// 21 March 1998 Kevin Karplus
//	Added clear_all().
// 30 March 1998 kevin Karplus
//	Moved some "globals" into NeuralNet.
// 2 May 1998 Kevin Karplus
//	Moved filename handling into Filenames/Filenames.h (and .cc)
// 21 May 2004 Sol Katzman
//	Added time functions
// Mon Jun 13 03:23:15 PDT 2005 Kevin Karplus
//	Picked up Jes Frellsen's addition of "design_chain"
// Sat Jun 18 10:58:46 PDT 2005 Kevin Karplus
//	Added BackgroundProbsByName and background_probs()
// Fri Jun 24 20:43:04 PDT 2005 Kevin Karplus
//	Replaced NN by vector NNs and made them private, with access
//	through  nn()
// Sun Jun 26 04:32:53 PDT 2005 Kevin Karplus
//	Added num_nns()
// Sat Jul  9 04:36:31 PDT 2005 Kevin Karplus
//	Changed design_chain to design_chains
//	Added clear_design_chains
// Thu Jul 14 22:02:13 PDT 2005 Kevin Karplus
//	added initialize_freeze and FreezeTheseColumns
// Thu Jul 21 17:55:20 PDT 2005 Kevin Karplus
//	added SequenceGenerator
// Sun Feb  5 02:41:02 PST 2006 Kevin Karplus
//	added ChangeTheseColumns
#endif